Figure 1.
Statistics of Illumina short read assembly quality.
The length distribution of de novo assembly for contigs and Unigenes is shown. 1, 200; 2, 300; 3, 400; 4, 500; 5, 600; 6, 700; 7, 800; 8, 900; 9, 1,000; 10, 1,100; 11, 1,200; 12, 1,300; 13, 1,400; 14, 1,500; 15, 1,600; 16,1,700; 17, 1,800; 18, 1,900; 19, 2,000; 20, 2,100; 21, 2,200; 22, 2,300; 23, 2,400; 24, 2,500; 25, 2,600; 26, 2,700; 27, 2,800; 28, 2,900; 29, 3,000; 30, >3,000.
Table 1.
Summary for the E. cf. polyphem transcriptome.
Figure 2.
GO annotations of non-redundant consensus sequences.
Best hits were aligned to the GO database, and 9,597 transcripts were assigned to at least one GO term. Most consensus sequences were grouped into three major functional categories, namely biological process, cellular component, and molecular function.
Figure 3.
COG annotations of putative proteins.
All putative proteins were aligned to the COG database and can be classified functionally into at least 25 molecular families. A, RNA processing and modification; B, Chromatin structure and dynamics; C, Energy production and conversion; D, Cell cycle control, cell division, chromosome partitioning; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme transport and metabolism; I, Lipid transport and metabolism; J, Translation, ribosomal structure and biogenesis; K, Transcription; L, Replication, recombination and repair; M, Cell wall/membrane/envelope biogenesis; N, Cell motility; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; W, Extracellular structures; Y, Nuclear structure; Z, Cytoskeleton.
Table 2.
Annotation of non-redundant consensus sequences.
Table 3.
Essential metabolic pathways annotated in the E. cf. polyphem transcriptome.
Table 4.
Enzymes involved in fatty acid biosynthesis and metabolism identified by annotation of the E. cf. polyphem transcriptome.
Table 5.
Enzymes involved in TAG biosynthesis identified by annotation of the E. cf. polyphem transcriptome.
Table 6.
Enzymes involved in chrysolaminarin biosynthesis and metabolism identified by annotation of the E. cf. polyphem transcriptome.
Figure 4.
Fatty acid biosynthesis pathway reconstructed based on the de novo assembly and annotation of E. cf. polyphem transcriptome.
Identified enzymes are shown in boxes and include: ACCase, acetyl-CoA carboxylase (EC: 6.4.1.2); MAT, malonyl-CoA ACP transacylase (EC: 2.3.1.39); KAS, 3-ketoacyl ACP synthase (KAS I, EC: 2.3.1.41; KASII, EC: 2.3.1.179; KAS III, EC: 2.3.1.180); KAR, 3-ketoacyl ACP reductase (EC: 1.1.1.100); HD, 3-hydroxy acyl-CoA dehydratase (EC: 4.2.1.-); EAR, enoyl-ACP reductase (NADH) (EC: 1.3.1.9); AAD, Δ9 Acyl-ACP desaturase (EC: 1.14.19.2); OAT, oleoyl-ACP thioesterase (EC: 3.1.2.14); Δ12D, Δ12(ω6)-desaturase (EC: 1.4.19.6); Δ15D, Δ15(ω3)-desaturase (EC: 1.4.19.-); Δ5D, Δ5- desaturase(EC: 1.14.99.-), Δ6D, Δ6- desaturase(EC: 1.14.99.-) and Δ6E, Δ6-elongase (EC: 6.21.3.-). The fatty acid biosynthesis pathway in E. cf. polyphem produces saturated, PA, palmitic acid (16:0) and SA, stearic acid (18:0), and unsaturated fatty acids OA, oleic acid (18:1ω9); LA, linoleic acid (18:2ω6); ALA, α-linolenic acid (18:3ω3); SDA, stearidonic acid (18:4ω3); ETA, eicosatetraenoic acid (20:4ω3) and EPA, eicosapentaenoic acid (20:5ω3).
Figure 5.
Triacylglycerol biosynthesis pathway reconstructed based on the de novo assembly and annotation of E. cf. polyphem transcriptome.
Identified enzymes are shown in boxes and include: GK, glycerol kinase (EC: 2.7.1.30); GPAT, glycerol-3-phosphate acyl transferase (EC: 2.3.1.15); AGPAT, lyso-phosphatidic acid acyl transferase (EC:2.3.1.51); PP, phosphatidate phosphatase (EC: 3.1.3.4); DGAT, diacylglycerol O-acyltransferase (EC: 2.3.1.20) and PDAT, phopholipid: diacyglycerol acyltransferase (EC 2.3.1.158). G-3-P, glycerol-3-phosphate; Lyso-PA, lyso-phosphatidic acid; PA, phosphatidic acid; DAG, diacylglycerol; PC, phosphatidylcholine and TAG, triacylglycerol.
Figure 6.
Carbohydrate accumulation properties of E. cf. polyphem.
(A) and (B) representative total carbohydrate and chrysolaminarin content for E. cf. polyphem cultured under nitrogen-replete (grey) and nitrogen-limited (black) conditions respectively.
Figure 7.
Chrysolaminarin biosynthesis and degradation pathway reconstructed based on the de novo assembly and annotation of E. cf. polyphem transcriptome.
Identified enzymes are shown in boxes and include: UGPase, UDP glucose pyrophosphorylase (EC: 2.7.7.9); UDPG, chrysolaminarin synthase (EC: 2.4.1.34); exo-Glu, exo-1,3-β-glucanase (EC: 3.2.1.58); endo-Glu, endo-1,3-β-glucanase (EC: 3.2.1.39) and BGL, β-glucosidases (EC: 3.2.1.21). G-1-P, glucose-1-phosphate; PPi, pyrophosphate.
Figure 8.
Glycolysis pathway reconstructed based on the de novo assembly and annotation of E. cf. polyphem transcriptome.
Identified enzymes are shown in boxes and include: HK, hexokinase (EC:2.7.1.1); GCK, glucokinase (EC: 2.7.1.2); G6PI, glucose-6-phosphate isomerase (EC: 5.3.1.9); PFK, phosphofructokinase-6 (EC: 2.7.1.11); FBA, fructose-bisphosphate aldolase (EC:4.1.2.13); TPI, triose-phosphate isomerase (EC: 5.3.1.1); GAPDH, glyceraldehyde-3-phosphate dehydrogenase (EC: 1.2.1.9, 1.2.1.12); GPDH, glycerol-3-phosphate dehydrogenase (EC:1.1.1.8); PGK, phosphoglycerate kinase (EC: 2.7.2.3); PGAM, phosphoglycerate mutase (EC: 5.4.2.1); ENO, enolase (EC: 4.2.1.11); PK, pyruvate kinase (EC: 2.7.1.40); PDC, pyruvate decarboxylase (EC: 4.1.1.1); ADH, alcohol dehydrogenase (EC: 1.1.1.1); PDHC, the pyruvate dehydrogenase complex consisting of PDHB, pyruvate dehydrogenase (acetyl-transferring) (EC: 1.2.4.1), DLAT, dihydrolipoamide acetyltransferase (EC: 2.3.1.12), DLD, dihydrolipoyl dehydrogenase (EC: 1.8.1.4). G-6-P, glucose-6-phosphate; F-6-P, fructose 6-phosphate; FBP, fructose-1,6-bisphosphate; GA3P, glyceraldehyde-3-phosphate; DHAP, dihydroxyacetone phosphate; G-3-P, glycerol-3-phosphate; 1,3BPG, 1, 3-bisphosphoglycerate; 3PG, 3-phosphoglycerate; 2PG, 2-phosphoglycerate; PEP, phosphoenolpyruvate.
Figure 9.
Carotenoid biosynthesis pathway reconstructed based on the de novo assembly and annotation of E. cf. polyphem transcriptome.
Identified enzymes are shown in boxes and include: GGPS, geranylgeranyl pyrophosphate synthase (EC: 2.5.1.1 2.5.1.10 2.5.1.29); PSY, phytoene synthase (EC: 2.5.1.32); PDS, phytoene dehydrogenase (EC: 1.14.99.-); ZDS, ζ-carotene desaturase (EC: 1.14.99.30); CrtY, lycopene beta-cyclase(EC: 1.14.-.-); CrtZ, β-carotene hydroxylase (EC: 1.14.13.-); ABA1, zeaxanthin epoxidase (EC: 1.14.13.90); VDE, violaxanthin de-epoxidase (EC: 1.10.99.3) and NSY, neoxanthin synthase (EC: 5.3.99.9). GA-3-P, glyceraldehyde-3-phosphate; IPP, isopentenyl pyrophosphate (C5); GGPP, geranylgeranyl pyrophosphate (C20).
Table 7.
Enzymes involved in carotenoid biosynthesis identified by annotation of the E. cf. polyphem transcriptome.